Tokyo-Kyoto-Hiroshima with kids & senior. Which JR pass and itinerary?

Hi,
Yes, a 14 day pass can serve you well, and you can take any JR route from one end of the country to the other. Since you mention you wish to travel 2 weeks by rail, there are a number of good places that are unique and both you and your kids will never forget them. Going to see Hakone through its round loop course makes a great day trip, plus when the weather is good the view of Mt. Fuji is wonderful. The Pass cannot take you all the way there but you can still get a discount through a Hakone Free Pass.

Going to see Takayama and Shirakawago are also very nice places to see the old Japan, and an overnight at a farmhouse will be unforgettable. Moving onward, Kanazawa has many nice places to see as well, including what is widely regarded as Japan's finest landscape garden, Kenrokuen.
Hiroshima offers a sobering but important stop for any traveler. In addition, Miyajima nearby is one of Japan's top attractions. The crown jewels of the country are undoubtedly in Kyoto and Nara though, both former capitals and steeped in old culture. Visiting nearby Himeji, which has Japan's finest castle, is also great and will add value to your Pass savings.
If that is still not enough, there are many places between or close to Hiroshima. Just a bit past Miyajima is Iwakuni with its conic historical bridge and mountaintop castle. Onomichi is famous for its temple tour and wildly ornate Kosanji Temple. Nearby Kurashiki is a famous own city for its canals, and Okayama also has its own castle and one of Japan's other Top 3 gardens, Korakuen. If your kids are itching to explore, then in Kagawa there is the Konpirasan Shrine in Kotohira, with a marvelous paved mountain hike.

There are really endless possibilities. Try browsing through some comprehensive tourist sites like:

http://www.jnto.go.jp